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Ray

Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data. Ray is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard.

Information

Usage

See versions of ray which are available

module avail ray

See the built-in help

Ray -help | less

Example batch job

Running Ray on two different nodes via MPI with a total of 15 CPUs:

#!/bin/env bash
#SBATCH -p batch
#SBATCH -n 15
#SBATCH -J ray
#SBATCH --nodes=2

module load ray/2.3.1

readonly DATADIR=~/data/bfusca
readonly OUTDIR=~/data/bfusca/ray-sept26

# mpirun gets the number of processors from SLURM
mpirun Ray -k 27 -p ${DATADIR}/1_S1_L001_R1_001_val_1.fastq.gz ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR}

Save in a file and submit using sbatch ray-mpi.sbatch.

Installation

Notes from the sysadmin during installation:

cd /tmp
git clone https://github.com/sebhtml/RayPlatform.git
git clone https://github.com/sebhtml/ray.git
cd ray
git checkout v2.3.1
scl enable devtoolset-1.1 bash
module load openmpi/1.8.2
make PREFIX=/export/apps/ray/2.3.1 HAVE_LIBZ=y HAVE_LIBBZ2=y
strip Ray
sudo mkdir -p /export/apps/ray/2.3.1
sudo chown -R aorth:aorth /export/apps/ray/2.3.1
make install
sudo chown -R root:root /export/apps/ray/2.3.1
ray-software.1411740064.txt.gz · Last modified: 2014/09/26 17:01 by aorth